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    vps-13D Ricin B-type lectin domain-containing protein [ Caenorhabditis elegans ]

    Gene ID: 173962, updated on 9-Dec-2024

    Summary

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    Official Symbol
    vps-13D
    Official Full Name
    Ricin B-type lectin domain-containing protein
    Primary source
    WormBase:WBGene00016120
    Locus tag
    CELE_C25H3.11
    See related
    AllianceGenome:WB:WBGene00016120
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Caenorhabditis elegans (strain: Bristol N2)
    Lineage
    Eukaryota; Metazoa; Ecdysozoa; Nematoda; Chromadorea; Rhabditida; Rhabditina; Rhabditomorpha; Rhabditoidea; Rhabditidae; Peloderinae; Caenorhabditis
    Summary
    Predicted to enable metal ion binding activity and transferase activity. Predicted to be involved in mitochondrion organization; protein retention in Golgi apparatus; and protein targeting to vacuole. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 4. Orthologous to human VPS13D (vacuolar protein sorting 13 homolog D). [provided by Alliance of Genome Resources, Dec 2024]
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    Genomic context

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    See vps-13D in Genome Data Viewer
    Location:
    chromosome: II
    Exon count:
    22
    Sequence:
    Chromosome: II; NC_003280.10 (5669771..5689040, complement)

    Chromosome II - NC_003280.10Genomic Context describing neighboring genes Neighboring gene Sensor histidine kinase Neighboring gene GST_C_6 domain-containing protein Neighboring gene PET117 cytochrome c oxidase chaperone Neighboring gene ncRNA Neighboring gene ncRNA Neighboring gene EASAFGDIIGELKGKGLGGRMRF-amide Neighboring gene pseudo Neighboring gene NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 5, mitochondrial

    Genomic regions, transcripts, and products

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    Genomic Sequence:
    NC_003280.10

    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. Genetic screen identifies non-mitochondrial proteins involved in the maintenance of mitochondrial homeostasis. Rolland S, et al. MicroPubl Biol, 2022. PMID 35622507, Free PMC Article
    2. Rapid and Efficient Identification of Caenorhabditis elegans Legacy Mutations Using Hawaiian SNP-Based Mapping and Whole-Genome Sequencing. Jaramillo-Lambert A, et al. G3 (Bethesda), 2015 Mar 4. PMID 25740937, Free PMC Article
    3. A map of the interactome network of the metazoan C. elegans. Li S, et al. Science, 2004 Jan 23. PMID 14704431, Free PMC Article
    4. OrthoList: a compendium of C. elegans genes with human orthologs. Shaye DD, et al. PLoS One, 2011. PMID 21647448, Free PMC Article
    5. OrthoList 2: A New Comparative Genomic Analysis of Human and Caenorhabditis elegans Genes. Kim W, et al. Genetics, 2018 Oct. PMID 30120140, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by WormBase

    Function Evidence Code Pubs
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in lipid transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitochondrion organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein retention in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein targeting to vacuole IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    Ricin B-type lectin domain-containing protein
    NP_001348703.1
    • Confirmed by transcript evidence
    NP_001348705.1
    • Confirmed by transcript evidence
    NP_001348706.1
    • Confirmed by transcript evidence
    NP_001368683.1
    • Partially confirmed by transcript evidence

    NCBI Reference Sequences (RefSeq)

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    Genome Annotation

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference assembly

    Genomic

    1. NC_003280.10 Reference assembly

      Range
      5669771..5689040 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001361857.4 → NP_001348706.1  Ricin B-type lectin domain-containing protein [Caenorhabditis elegans]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A2K5ATR9
      Conserved Domains (5) summary
      COG5043
      Location:1 → 2079
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      cd00161
      Location:2533 → 2637
      RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
      pfam06650
      Location:2204 → 2478
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam16908
      Location:145 → 369
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:2896 → 3026
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    2. NM_001361860.2 → NP_001348703.1  Ricin B-type lectin domain-containing protein [Caenorhabditis elegans]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A2K5ATR5
      Conserved Domains (5) summary
      COG5043
      Location:1 → 2091
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      cd00161
      Location:2545 → 2649
      RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
      pfam06650
      Location:2216 → 2490
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam16908
      Location:145 → 369
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:2908 → 3038
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    3. NM_001361858.3 → NP_001348705.1  Ricin B-type lectin domain-containing protein [Caenorhabditis elegans]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A2K5ATQ8
      Conserved Domains (5) summary
      COG5043
      Location:1 → 2081
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      cd00161
      Location:2535 → 2639
      RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
      pfam06650
      Location:2206 → 2480
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam16908
      Location:145 → 369
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:2898 → 3028
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal

    4. NM_001381432.1 → NP_001368683.1  Ricin B-type lectin domain-containing protein [Caenorhabditis elegans]

      Status: REVIEWED

      UniProtKB/TrEMBL
      A0A2K5ATQ3
      Conserved Domains (5) summary
      COG5043
      Location:1 → 2089
      MRS6; Vacuolar protein sorting-associated protein [Intracellular trafficking and secretion]
      cd00161
      Location:2543 → 2647
      RICIN; Ricin-type beta-trefoil; Carbohydrate-binding domain formed from presumed gene triplication. The domain is found in a variety of molecules serving diverse functions such as enzymatic activity, inhibitory toxicity and signal transduction. Highly specific ...
      pfam06650
      Location:2214 → 2488
      SHR-BD; SHR-binding domain of vacuolar-sorting associated protein 13
      pfam16908
      Location:145 → 369
      VPS13; Vacuolar sorting-associated protein 13, N-terminal
      pfam16909
      Location:2919 → 3036
      VPS13_C; Vacuolar-sorting-associated 13 protein C-terminal
    Nucleotide Protein
    Heading Accession and Version

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